From 502fc46566815c5f71178405ccd9eb777ce07e51 Mon Sep 17 00:00:00 2001 From: Andreas Tille Date: Thu, 1 Sep 2016 08:01:23 +0000 Subject: [PATCH] Import htslib_1.3.1-3.debian.tar.xz [dgit import tarball htslib 1.3.1-3 htslib_1.3.1-3.debian.tar.xz] --- README.source | 34 ++ changelog | 112 ++++++ compat | 1 + control | 85 +++++ copyright | 117 +++++++ gbp.conf | 15 + htslib-test.install | 7 + libhts-dev.install | 6 + libhts1.install | 2 + libhts1.lintian-overrides | 2 + libhts1.symbols | 639 ++++++++++++++++++++++++++++++++++ patches/define_PATH_MAX.patch | 37 ++ patches/literal_version.patch | 16 + patches/series | 2 + rules | 38 ++ source/format | 1 + source/options | 2 + tabix.install | 2 + tabix.links | 1 + tabix.lintian-overrides | 3 + tabix.manpages | 1 + tests/control | 3 + tests/run-unit-test | 19 + upstream/tabix.edam | 16 + watch | 3 + 25 files changed, 1164 insertions(+) create mode 100644 README.source create mode 100644 changelog create mode 100644 compat create mode 100644 control create mode 100644 copyright create mode 100644 gbp.conf create mode 100644 htslib-test.install create mode 100755 libhts-dev.install create mode 100755 libhts1.install create mode 100644 libhts1.lintian-overrides create mode 100644 libhts1.symbols create mode 100644 patches/define_PATH_MAX.patch create mode 100644 patches/literal_version.patch create mode 100644 patches/series create mode 100755 rules create mode 100644 source/format create mode 100644 source/options create mode 100644 tabix.install create mode 100644 tabix.links create mode 100644 tabix.lintian-overrides create mode 100644 tabix.manpages create mode 100644 tests/control create mode 100644 tests/run-unit-test create mode 100644 upstream/tabix.edam create mode 100644 watch diff --git a/README.source b/README.source new file mode 100644 index 0000000..25e2600 --- /dev/null +++ b/README.source @@ -0,0 +1,34 @@ +Since this Git repository does not follow the usual Debian Med +workflow it is documented here, how the package can be updated: + + 1. in the master branch, pull the upstream master branch and its tags. + + git checkout master + git pull https://github.com/samtools/htslib --tags + + Remark: If this pull fails with a lot of stuff to merge you might + have some ~/.gitconfig that breaks the pull above. Please try to + deactivate it for the moment. + + 2. Merge the tag in the debian/unstable branch + + git checkout debian/unstable ; git merge + + 3. download the upstream tarball + + uscan --force-download + + 4. Register the upstream tarball in the pristine-tar branch directly with + the pristine-tar command directly (stay in master branch when doing this) + + pristine-tar commit ../htslib_.orig.tar.gz + + 5. Update the packaging files, build with gbp - debian-branch and + upstream-branch are properly set in debian/gbp.conf + +According to Charles Plessy this workflow has the advantage to propose +upstream via pull requests on GitHub. The Debian Med policy currently +does only contain a short paragraph to mention the derived workflow: + + http://debian-med.alioth.debian.org/docs/policy.html#git-without-tarball + diff --git a/changelog b/changelog new file mode 100644 index 0000000..4939412 --- /dev/null +++ b/changelog @@ -0,0 +1,112 @@ +htslib (1.3.1-3) unstable; urgency=medium + + * Fix build on hurd (thanks for the patch to Svante Signell + ) + Closes: #836190 + * Add myself to uploaders + + -- Andreas Tille Thu, 01 Sep 2016 10:01:23 +0200 + +htslib (1.3.1-2) unstable; urgency=medium + + [ Canberk Koç ] + * Team upload. + * Autopktest added + + [ Andreas Tille ] + * hardening=+bindnow + + -- Canberk Koç Wed, 03 Aug 2016 04:21:17 +0300 + +htslib (1.3.1-1) unstable; urgency=medium + + 36bf59a Merge tag '1.3.1' into debian/unstable + 559f8b4 Remove add_largefile.patch, applied upstream. + 7163afb Update symbols file. Missing _vcf_parse_format@Base and fai_read@Base. + c2c1df3 Build-depend on libcurl4-gnutls-dev and libssl-dev. + 3b219b8 Enable libcurl. + 9101580 Conforms to the Policy version 3.9.8. + + -- Charles Plessy Mon, 25 Apr 2016 22:28:11 +0900 + +htslib (1.3-2) unstable; urgency=medium + + * Team upload + + [ Steffen Moeller and Jon Ison ] + * Introduction of EDAM annotation + + [ Sascha Steinbiss ] + * Include upstream patch for large file support + * Run configure as part of the build + + -- Sascha Steinbiss Mon, 08 Feb 2016 16:46:35 +0000 + +htslib (1.3-1) unstable; urgency=medium + + * Team upload + * New upstream version + * Ignore metadata files different between git and tarball + + -- Sascha Steinbiss Sat, 30 Jan 2016 12:16:06 +0000 + +htslib (1.2.1-2) unstable; urgency=medium + + * Team upload + * Enable build on hurd-i386 + Closes: #793512 + * More verbose description vor -dev and -test package + * Fix lintian override + * Verified Mayhem bug report which is solved in this version + Closes: #716376 + + -- Andreas Tille Wed, 09 Dec 2015 17:00:47 +0100 + +htslib (1.2.1-1) unstable; urgency=medium + + 0662716 Merge tag '1.2.1' into debian/unstable + 084f27d Install NEWS as upstream changelog. + 316fb96 Override a Lintian false positive. + 3363679 Clean test directory. + 69bf167 Corrected a typo in tabix description. + + -- Charles Plessy Mon, 25 May 2015 13:35:03 +0900 + +htslib (1.1-1) unstable; urgency=medium + + 1357fbd Merge tag '1.1' into debian/unstable + 87549cd Updated symbols file. One symbol is missing. + 873ea9b Removed orphan paragraph in machine-readable copyright file. + 49de2b9 Allow parallel build. + 7fe3bb5 Normalise control file (VCS-Browser, Pre-Depends). + 0e5e9e6 Conforms to Policy 3.9.6. + + -- Charles Plessy Wed, 24 Sep 2014 21:24:11 +0900 + +htslib (1.0-2) unstable; urgency=medium + + Uploaded to unstable (see previous changelog from experimental). + + -- Charles Plessy Tue, 16 Sep 2014 20:27:04 +0900 + +htslib (1.0-1) experimental; urgency=low + + cc559b8 Merged with upstream's master branch. + 74b9d7b Build on the master branch. + 04815a7 New major version (libhts0 -> libhts1). + 98c18ca Updated symbols file. + 22fef0c Install pkgconfig file. + 420896b Override PACKAGE_VERSION to avoid tags with a slash in the name. + 79b5d4e Use the Debian package version as PACKAGE_VERSION. + 72b5c4a Finally use the 3.0 (quilt) format in single-debian-patch mode. + d870946 Adjusted substitution variables following dpkg's warnings. + 9469458 Removed debug command accidentally introduced. + 8c7f7d4 Replace the old tabix package from the tabix source package. + + -- Charles Plessy Sun, 17 Aug 2014 20:12:28 +0900 + +htslib (0.2.0~rc3-1) unstable; urgency=low + + * Initial release. (Closes: #729282) + + -- Charles Plessy Sat, 16 Nov 2013 15:35:03 +0900 diff --git a/compat b/compat new file mode 100644 index 0000000..ec63514 --- /dev/null +++ b/compat @@ -0,0 +1 @@ +9 diff --git a/control b/control new file mode 100644 index 0000000..c5c13e5 --- /dev/null +++ b/control @@ -0,0 +1,85 @@ +Source: htslib +Maintainer: Debian Med Packaging Team +Uploaders: Charles Plessy , + Andreas Tille +Section: science +Priority: optional +Build-Depends: debhelper (>= 9), + dh-exec, + libcurl4-gnutls-dev, + libssl-dev, + zlib1g-dev, + autoconf +Standards-Version: 3.9.8 +Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/htslib.git +Vcs-Git: https://anonscm.debian.org/git/debian-med/htslib.git -b debian/unstable +Homepage: https://github.com/samtools/htslib + +Package: libhts1 +Architecture: any +Multi-Arch: same +Section: libs +Depends: ${shlibs:Depends}, + ${misc:Depends} +Pre-Depends: ${misc:Pre-Depends} +Description: C library for high-throughput sequencing data formats + HTSlib is an implementation of a unified C library for accessing common file + formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call + Format), used for high-throughput sequencing data, and is the core library + used by samtools and bcftools. HTSlib only depends on zlib. It is known to be + compatible with gcc, g++ and clang. + . + HTSlib implements a generalized BAM (binary SAM) index, with file extension + ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the + new index and then for the old if the new index is absent. + +Package: libhts-dev +Architecture: any +Multi-Arch: same +Section: libdevel +Depends: libhts1 (= ${binary:Version}), + ${misc:Depends} +Description: Development files for the HTSlib + HTSlib is an implementation of a unified C library for accessing common file + formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call + Format), used for high-throughput sequencing data, and is the core library + used by samtools and bcftools. HTSlib only depends on zlib. It is known to be + compatible with gcc, g++ and clang. + . + HTSlib implements a generalized BAM (binary SAM) index, with file extension + ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the + new index and then for the old if the new index is absent. + . + This package contains development files for the HTSlib: headers, static + library, manual pages, etc. + +Package: htslib-test +Architecture: all +Depends: ${misc:Depends}, + ${perl:Depends} +Description: Test data for HTSlib + HTSlib is an implementation of a unified C library for accessing common file + formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call + Format), used for high-throughput sequencing data, and is the core library + used by samtools and bcftools. HTSlib only depends on zlib. It is known to be + compatible with gcc, g++ and clang. + . + HTSlib implements a generalized BAM (binary SAM) index, with file extension + ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the + new index and then for the old if the new index is absent. + . + This package contains test files and scripts for the HTSlib. + +Package: tabix +Architecture: any +Depends: ${misc:Depends}, + ${shlibs:Depends} +Description: generic indexer for TAB-delimited genome position files + Tabix indexes files where some columns indicate sequence coordinates: name + (usually a chromosome), start and stop. The input data file must be position + sorted and compressed by bgzip (provided in this package), which has a gzip + like interface. After indexing, tabix is able to quickly retrieve data lines by + chromosomal coordinates. Fast data retrieval also works over network if an URI + is given as a file name. + . + This version of tabix is built from the HTSlib source. diff --git a/copyright b/copyright new file mode 100644 index 0000000..a923ec3 --- /dev/null +++ b/copyright @@ -0,0 +1,117 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Source: https://github.com/samtools/htslib/archive/1.3.1.tar.gz + +Files: * +Copyright: © 2012-2016 Genome Research Ltd. + © 2008-2013 Broad Institute / Massachusetts Institute of Technology + © The Wellcome Trust Sanger Institute + © 2008-2012 by Attractive Chaos +License: MIT + +Files: cram/* +Copyright: © 2012-2014 Genome Research Ltd. + © 1995-2003 MEDICAL RESEARCH COUNCIL +License: Various_BSD-3-Clause + The files in the 'cram' directory are under one or both of the following + licenses. + . + --------------------------------------------------------------------------- + . + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are met: + . + 1. Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + . + 2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + . + 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger + Institute nor the names of its contributors may be used to endorse or promote + products derived from this software without specific prior written permission. + . + THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND + ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE + FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL + DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR + SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER + CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + . + --------------------------------------------------------------------------- + . + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are met: + . + 1 Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + . + 2 Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + . + 3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF + MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or + promote products derived from this software without specific prior written + permission. + . + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR + ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON + ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +Files: md5.c +Copyright: No copyright is claimed +License: solar-MD5 + This is an OpenSSL-compatible implementation of the RSA Data Security, Inc. + MD5 Message-Digest Algorithm (RFC 1321). + . + Homepage: + http://openwall.info/wiki/people/solar/software/public-domain-source-code/md5 + . + Author: + Alexander Peslyak, better known as Solar Designer + . + This software was written by Alexander Peslyak in 2001. No copyright is + claimed, and the software is hereby placed in the public domain. + In case this attempt to disclaim copyright and place the software in the + public domain is deemed null and void, then the software is + Copyright (c) 2001 Alexander Peslyak and it is hereby released to the + general public under the following terms: + . + Redistribution and use in source and binary forms, with or without + modification, are permitted. + . + There's ABSOLUTELY NO WARRANTY, express or implied. + +License: MIT + Permission is hereby granted, free of charge, to any person obtaining + a copy of this software and associated documentation files (the + "Software"), to deal in the Software without restriction, including + without limitation the rights to use, copy, modify, merge, publish, + distribute, sublicense, and/or sell copies of the Software, and to + permit persons to whom the Software is furnished to do so, subject to + the following conditions: + . + The above copyright notice and this permission notice shall be + included in all copies or substantial portions of the Software. + . + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS + BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN + ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. + diff --git a/gbp.conf b/gbp.conf new file mode 100644 index 0000000..533b176 --- /dev/null +++ b/gbp.conf @@ -0,0 +1,15 @@ +# This package uses pristine-tar, and does not follow the canonical layout of git-buildpackage. + +[DEFAULT] +# the default branch for upstream sources: +upstream-branch = master +# the default branch for the debian patch: +debian-branch = debian/unstable +# the default tag formats used: +upstream-tag = %(version)s +# use pristine-tar: +pristine-tar = True + +[dch] +# include 7 digits of the commit id in the changelog enty: +id-length = 7 diff --git a/htslib-test.install b/htslib-test.install new file mode 100644 index 0000000..a9d8290 --- /dev/null +++ b/htslib-test.install @@ -0,0 +1,7 @@ +test/* /usr/share/htslib-test/test +cram/*.h /usr/share/htslib-test/cram +cram/*.c /usr/share/htslib-test/cram +Makefile /usr/share/htslib-test +*.mk /usr/share/htslib-test +*.c /usr/share/htslib-test +*.h /usr/share/htslib-test diff --git a/libhts-dev.install b/libhts-dev.install new file mode 100755 index 0000000..87e7d23 --- /dev/null +++ b/libhts-dev.install @@ -0,0 +1,6 @@ +#! /usr/bin/dh-exec +usr/include/* usr/include +usr/lib/${DEB_HOST_MULTIARCH}/*.a usr/lib/${DEB_HOST_MULTIARCH} +usr/lib/${DEB_HOST_MULTIARCH}/*.so usr/lib/${DEB_HOST_MULTIARCH} +usr/share/man/man5/* usr/share/man/man5 +usr/lib/${DEB_HOST_MULTIARCH}/pkgconfig/htslib.pc usr/lib/${DEB_HOST_MULTIARCH}/pkgconfig diff --git a/libhts1.install b/libhts1.install new file mode 100755 index 0000000..659d59c --- /dev/null +++ b/libhts1.install @@ -0,0 +1,2 @@ +#! /usr/bin/dh-exec +usr/lib/${DEB_HOST_MULTIARCH}/libhts.so.* usr/lib/${DEB_HOST_MULTIARCH} diff --git a/libhts1.lintian-overrides b/libhts1.lintian-overrides new file mode 100644 index 0000000..e53f49f --- /dev/null +++ b/libhts1.lintian-overrides @@ -0,0 +1,2 @@ +# False positive +libhts1: spelling-error-in-binary usr/lib/x86_64-linux-gnu/libhts.so.* compres compress diff --git a/libhts1.symbols b/libhts1.symbols new file mode 100644 index 0000000..15a90ae --- /dev/null +++ b/libhts1.symbols @@ -0,0 +1,639 @@ +libhts.so.1 libhts1 #MINVER# + _reader_next_line@Base 1.0 + _regidx_build_index@Base 1.2.1 +#MISSING: 1.3.1# _vcf_parse_format@Base 1.0 + bam_aux2A@Base 1.0 + bam_aux2Z@Base 1.0 + bam_aux2f@Base 1.0 + bam_aux2i@Base 1.0 + bam_aux_append@Base 1.0 + bam_aux_del@Base 1.0 + bam_aux_get@Base 1.0 + bam_cigar2qlen@Base 1.0 + bam_cigar2rlen@Base 1.0 + bam_construct_seq@Base 1.0 + bam_copy1@Base 1.0 + bam_destroy1@Base 1.0 + bam_dup1@Base 1.0 + bam_endpos@Base 1.0 + bam_flag2str@Base 1.0 + bam_hdr_destroy@Base 1.0 + bam_hdr_dup@Base 1.0 + bam_hdr_init@Base 1.0 + bam_hdr_read@Base 1.0 + bam_hdr_write@Base 1.0 + bam_header_to_cram@Base 1.0 + bam_index_build@Base 1.0 + bam_init1@Base 1.0 + bam_mplp_auto@Base 1.0 + bam_mplp_destroy@Base 1.0 + bam_mplp_init@Base 1.0 + bam_mplp_init_overlaps@Base 1.0 + bam_mplp_set_maxcnt@Base 1.0 + bam_name2id@Base 1.0 + bam_plp_auto@Base 1.0 + bam_plp_destroy@Base 1.0 + bam_plp_init@Base 1.0 + bam_plp_init_overlaps@Base 1.0 + bam_plp_next@Base 1.0 + bam_plp_push@Base 1.0 + bam_plp_reset@Base 1.0 + bam_plp_set_maxcnt@Base 1.0 + bam_read1@Base 1.0 + bam_str2flag@Base 1.0 + bam_write1@Base 1.0 + bcf_add_filter@Base 1.0 + bcf_add_id@Base 1.3 + bcf_calc_ac@Base 1.0 + bcf_clear@Base 1.0 + bcf_copy@Base 1.2.1 + bcf_destroy@Base 1.0 + bcf_dup@Base 1.0 + bcf_empty@Base 1.3 + bcf_enc_vchar@Base 1.0 + bcf_enc_vfloat@Base 1.0 + bcf_enc_vint@Base 1.0 + bcf_float_missing@Base 1.0 + bcf_float_vector_end@Base 1.0 + bcf_fmt_array@Base 1.0 + bcf_fmt_sized_array@Base 1.0 + bcf_get_fmt@Base 1.0 + bcf_get_fmt_id@Base 1.1 + bcf_get_format_string@Base 1.0 + bcf_get_format_values@Base 1.0 + bcf_get_info@Base 1.0 + bcf_get_info_id@Base 1.1 + bcf_get_info_values@Base 1.0 + bcf_get_variant_type@Base 1.0 + bcf_get_variant_types@Base 1.0 + bcf_gt_type@Base 1.0 + bcf_has_filter@Base 1.0 + bcf_hdr_add_hrec@Base 1.0 + bcf_hdr_add_sample@Base 1.0 + bcf_hdr_append@Base 1.0 + bcf_hdr_check_sanity@Base 1.0 + bcf_hdr_combine@Base 1.0 + bcf_hdr_destroy@Base 1.0 + bcf_hdr_dup@Base 1.0 + bcf_hdr_fmt_text@Base 1.0 + bcf_hdr_get_hrec@Base 1.0 + bcf_hdr_get_version@Base 1.0 + bcf_hdr_id2int@Base 1.0 + bcf_hdr_init@Base 1.0 + bcf_hdr_merge@Base 1.3 + bcf_hdr_parse@Base 1.0 + bcf_hdr_parse_line@Base 1.0 + bcf_hdr_parse_sample_line@Base 1.0 + bcf_hdr_printf@Base 1.0 + bcf_hdr_read@Base 1.0 + bcf_hdr_register_hrec@Base 1.0 + bcf_hdr_remove@Base 1.0 + bcf_hdr_seqnames@Base 1.0 + bcf_hdr_set@Base 1.0 + bcf_hdr_set_samples@Base 1.0 + bcf_hdr_set_version@Base 1.0 + bcf_hdr_subset@Base 1.0 + bcf_hdr_sync@Base 1.0 + bcf_hdr_write@Base 1.0 + bcf_header_debug@Base 1.0 + bcf_hrec_add_key@Base 1.0 + bcf_hrec_debug@Base 1.0 + bcf_hrec_destroy@Base 1.0 + bcf_hrec_dup@Base 1.0 + bcf_hrec_find_key@Base 1.0 + bcf_hrec_format@Base 1.0 + bcf_hrec_set_val@Base 1.0 + bcf_index@Base 1.0 + bcf_index_build2@Base 1.3 + bcf_index_build@Base 1.0 + bcf_index_load2@Base 1.3 + bcf_init@Base 1.0 + bcf_is_snp@Base 1.0 + bcf_read@Base 1.0 + bcf_readrec@Base 1.0 + bcf_remove_allele_set@Base 1.3 + bcf_remove_alleles@Base 1.0 + bcf_remove_filter@Base 1.0 + bcf_sr_add_reader@Base 1.0 + bcf_sr_destroy@Base 1.0 + bcf_sr_init@Base 1.0 + bcf_sr_next_line@Base 1.0 + bcf_sr_regions_destroy@Base 1.0 + bcf_sr_regions_flush@Base 1.0 + bcf_sr_regions_init@Base 1.0 + bcf_sr_regions_next@Base 1.0 + bcf_sr_regions_overlap@Base 1.0 + bcf_sr_regions_seek@Base 1.0 + bcf_sr_remove_reader@Base 1.0 + bcf_sr_seek@Base 1.0 + bcf_sr_set_regions@Base 1.0 + bcf_sr_set_samples@Base 1.0 + bcf_sr_set_targets@Base 1.0 + bcf_sr_strerror@Base 1.2.1 + bcf_subset@Base 1.0 + bcf_subset_format@Base 1.0 + bcf_sweep_bwd@Base 1.0 + bcf_sweep_destroy@Base 1.0 + bcf_sweep_fwd@Base 1.0 + bcf_sweep_hdr@Base 1.0 + bcf_sweep_init@Base 1.0 + bcf_translate@Base 1.0 + bcf_trim_alleles@Base 1.0 + bcf_type_shift@Base 1.0 + bcf_unpack@Base 1.0 + bcf_update_alleles@Base 1.0 + bcf_update_alleles_str@Base 1.0 + bcf_update_filter@Base 1.0 + bcf_update_format@Base 1.0 + bcf_update_format_string@Base 1.0 + bcf_update_id@Base 1.0 + bcf_update_info@Base 1.0 + bcf_write@Base 1.0 + bgzf_check_EOF@Base 1.0 + bgzf_close@Base 1.0 + bgzf_compress@Base 1.3 + bgzf_dopen@Base 1.0 + bgzf_flush@Base 1.0 + bgzf_flush_try@Base 1.0 + bgzf_getc@Base 1.0 + bgzf_getline@Base 1.0 + bgzf_hopen@Base 1.0 + bgzf_index_add_block@Base 1.0 + bgzf_index_build_init@Base 1.0 + bgzf_index_destroy@Base 1.0 + bgzf_index_dump@Base 1.0 + bgzf_index_load@Base 1.0 + bgzf_is_bgzf@Base 1.0 + bgzf_mt@Base 1.0 + bgzf_open@Base 1.0 + bgzf_raw_read@Base 1.0 + bgzf_raw_write@Base 1.0 + bgzf_read@Base 1.0 + bgzf_read_block@Base 1.0 + bgzf_seek@Base 1.0 + bgzf_set_cache_size@Base 1.0 + bgzf_useek@Base 1.0 + bgzf_utell@Base 1.0 + bgzf_write@Base 1.0 + cram_beta_decode_char@Base 1.0 + cram_beta_decode_free@Base 1.0 + cram_beta_decode_init@Base 1.0 + cram_beta_decode_int@Base 1.0 + cram_beta_encode_char@Base 1.0 + cram_beta_encode_free@Base 1.0 + cram_beta_encode_init@Base 1.0 + cram_beta_encode_int@Base 1.0 + cram_beta_encode_store@Base 1.0 + cram_block_append@Base 1.3 + cram_block_compression_hdr_decoder2encoder@Base 1.3 + cram_block_compression_hdr_set_rg@Base 1.3 + cram_block_get_comp_size@Base 1.3 + cram_block_get_content_id@Base 1.3 + cram_block_get_content_type@Base 1.3 + cram_block_get_crc32@Base 1.3 + cram_block_get_data@Base 1.3 + cram_block_get_offset@Base 1.3 + cram_block_get_size@Base 1.3 + cram_block_get_uncomp_size@Base 1.3 + cram_block_method2str@Base 1.0 + cram_block_set_comp_size@Base 1.3 + cram_block_set_content_id@Base 1.3 + cram_block_set_crc32@Base 1.3 + cram_block_set_data@Base 1.3 + cram_block_set_offset@Base 1.3 + cram_block_set_size@Base 1.3 + cram_block_set_uncomp_size@Base 1.3 + cram_block_size@Base 1.3 + cram_block_update_size@Base 1.3 + cram_byte_array_len_decode@Base 1.0 + cram_byte_array_len_decode_free@Base 1.0 + cram_byte_array_len_decode_init@Base 1.0 + cram_byte_array_len_encode@Base 1.0 + cram_byte_array_len_encode_free@Base 1.0 + cram_byte_array_len_encode_init@Base 1.0 + cram_byte_array_len_encode_store@Base 1.0 + cram_byte_array_stop_decode_block@Base 1.0 + cram_byte_array_stop_decode_free@Base 1.0 + cram_byte_array_stop_decode_init@Base 1.0 + cram_byte_array_stop_encode@Base 1.0 + cram_byte_array_stop_encode_free@Base 1.0 + cram_byte_array_stop_encode_init@Base 1.0 + cram_byte_array_stop_encode_store@Base 1.0 + cram_close@Base 1.0 + cram_codec_decoder2encoder@Base 1.3 + cram_codec_to_id@Base 1.2.1 + cram_compress_block@Base 1.0 + cram_container_get_landmarks@Base 1.3 + cram_container_get_length@Base 1.3 + cram_container_get_num_blocks@Base 1.3 + cram_container_is_empty@Base 1.3 + cram_container_set_landmarks@Base 1.3 + cram_container_set_length@Base 1.3 + cram_container_set_num_blocks@Base 1.3 + cram_container_size@Base 1.3 + cram_content_type2str@Base 1.0 + cram_copy_slice@Base 1.3 + cram_decode_TD@Base 1.0 + cram_decode_compression_header@Base 1.0 + cram_decode_estimate_sizes@Base 1.3 + cram_decode_slice@Base 1.0 + cram_decode_slice_header@Base 1.0 + cram_decode_slice_mt@Base 1.0 + cram_decode_slice_thread@Base 1.0 + cram_decoder_init@Base 1.0 + cram_dependent_data_series@Base 1.2.1 + cram_dopen@Base 1.0 + cram_encode_compression_header@Base 1.0 + cram_encode_container@Base 1.0 + cram_encode_slice_header@Base 1.0 + cram_encoder_init@Base 1.0 + cram_encoding2str@Base 1.0 + cram_eof@Base 1.0 + cram_external_decode_char@Base 1.0 + cram_external_decode_free@Base 1.0 + cram_external_decode_init@Base 1.0 + cram_external_decode_int@Base 1.0 + cram_external_encode_char@Base 1.2.1 + cram_external_encode_free@Base 1.0 + cram_external_encode_init@Base 1.0 + cram_external_encode_int@Base 1.2.1 + cram_external_encode_store@Base 1.0 + cram_fd_get_fp@Base 1.3 + cram_fd_get_header@Base 1.3 + cram_fd_get_version@Base 1.3 + cram_fd_set_fp@Base 1.3 + cram_fd_set_header@Base 1.3 + cram_fd_set_version@Base 1.3 + cram_flush@Base 1.0 + cram_flush_container@Base 1.0 + cram_flush_container_mt@Base 1.0 + cram_flush_thread@Base 1.0 + cram_free_block@Base 1.0 + cram_free_compression_header@Base 1.0 + cram_free_container@Base 1.0 + cram_free_file_def@Base 1.0 + cram_free_slice@Base 1.0 + cram_free_slice_header@Base 1.0 + cram_gamma_decode@Base 1.0 + cram_gamma_decode_free@Base 1.0 + cram_gamma_decode_init@Base 1.0 + cram_get_bam_seq@Base 1.0 + cram_get_ref@Base 1.0 + cram_get_seq@Base 1.0 + cram_header_to_bam@Base 1.0 + cram_huffman_decode_char0@Base 1.0 + cram_huffman_decode_char@Base 1.0 + cram_huffman_decode_free@Base 1.0 + cram_huffman_decode_init@Base 1.0 + cram_huffman_decode_int0@Base 1.0 + cram_huffman_decode_int@Base 1.0 + cram_huffman_decode_null@Base 1.3 + cram_huffman_encode_char0@Base 1.0 + cram_huffman_encode_char@Base 1.0 + cram_huffman_encode_free@Base 1.0 + cram_huffman_encode_init@Base 1.0 + cram_huffman_encode_int0@Base 1.0 + cram_huffman_encode_int@Base 1.0 + cram_huffman_encode_store@Base 1.0 + cram_index_build@Base 1.0 + cram_index_free@Base 1.0 + cram_index_load@Base 1.0 + cram_index_query@Base 1.0 + cram_load_reference@Base 1.0 + cram_major_vers@Base 1.3 + cram_minor_vers@Base 1.3 + cram_new_block@Base 1.0 + cram_new_compression_header@Base 1.0 + cram_new_container@Base 1.0 + cram_new_metrics@Base 1.0 + cram_new_slice@Base 1.0 + cram_open@Base 1.0 + cram_put_bam_seq@Base 1.0 + cram_read_SAM_hdr@Base 1.0 + cram_read_block@Base 1.0 + cram_read_container@Base 1.0 + cram_read_file_def@Base 1.0 + cram_read_slice@Base 1.0 + cram_ref_decr@Base 1.0 + cram_ref_incr@Base 1.0 + cram_ref_load@Base 1.0 + cram_seek@Base 1.0 + cram_seek_to_refpos@Base 1.0 + cram_set_header@Base 1.0 + cram_set_option@Base 1.0 + cram_set_voption@Base 1.0 + cram_slice_hdr_get_num_blocks@Base 1.3 + cram_stats_add@Base 1.0 + cram_stats_create@Base 1.0 + cram_stats_del@Base 1.0 + cram_stats_dump@Base 1.0 + cram_stats_encoding@Base 1.0 + cram_stats_free@Base 1.0 + cram_store_container@Base 1.3 + cram_subexp_decode@Base 1.0 + cram_subexp_decode_free@Base 1.0 + cram_subexp_decode_init@Base 1.0 + cram_transcode_rg@Base 1.3 + cram_uncompress_block@Base 1.0 + cram_write_SAM_hdr@Base 1.0 + cram_write_block@Base 1.0 + cram_write_container@Base 1.0 + cram_write_file_def@Base 1.0 + debug_buffer@Base 1.0 + debug_buffers@Base 1.0 + expand_cache_path@Base 1.0 + fai_build@Base 1.0 + fai_build_core@Base 1.0 + fai_destroy@Base 1.0 + fai_fetch@Base 1.0 + fai_load@Base 1.0 +#MISSING: 1.3.1# fai_read@Base 1.0 + fai_save@Base 1.0 + faidx_fetch_nseq@Base 1.2.1 + faidx_fetch_seq@Base 1.0 + faidx_has_seq@Base 1.0 + faidx_iseq@Base 1.1 + faidx_nseq@Base 1.1 + faidx_seq_len@Base 1.1 + file_exists@Base 1.0 + file_size@Base 1.0 + find_file_url@Base 1.0 + find_path@Base 1.3 + flen@Base 1.0 + hclose@Base 1.0 + hclose_abruptly@Base 1.0 + hdopen@Base 1.0 + hfile_add_scheme_handler@Base 1.3 + hfile_always_local@Base 1.3 + hfile_always_remote@Base 1.3 + hfile_destroy@Base 1.0 + hfile_init@Base 1.0 + hfile_oflags@Base 1.0 + hfile_plugin_init_libcurl@Base 1.3.1 + hfile_plugin_init_net@Base 1.3 + hflush@Base 1.0 + hgetc2@Base 1.0 + hisremote@Base 1.2.1 + hopen@Base 1.0 + hopen_libcurl@Base 1.3.1 + hopen_net@Base 1.0 + hpeek@Base 1.0 + hputc2@Base 1.0 + hputs2@Base 1.0 + hread2@Base 1.0 + hrec_add_idx@Base 1.0 + hseek@Base 1.0 + hts_close@Base 1.0 + hts_detect_format@Base 1.2.1 + hts_file_type@Base 1.0 + hts_format_description@Base 1.2.1 + hts_format_file_extension@Base 1.3 + hts_get_bgzfp@Base 1.0 + hts_get_format@Base 1.2.1 + hts_getline@Base 1.0 + hts_hopen@Base 1.2.1 + hts_idx_destroy@Base 1.0 + hts_idx_finish@Base 1.0 + hts_idx_get_meta@Base 1.0 + hts_idx_get_n_no_coor@Base 1.0 + hts_idx_get_stat@Base 1.0 + hts_idx_getfn@Base 1.0 + hts_idx_init@Base 1.0 + hts_idx_load2@Base 1.3 + hts_idx_load@Base 1.0 + hts_idx_push@Base 1.0 + hts_idx_save@Base 1.0 + hts_idx_save_as@Base 1.3 + hts_idx_seqnames@Base 1.0 + hts_idx_set_meta@Base 1.0 + hts_itr_destroy@Base 1.0 + hts_itr_next@Base 1.0 + hts_itr_query@Base 1.0 + hts_itr_querys@Base 1.0 + hts_md5_destroy@Base 1.3 + hts_md5_final@Base 1.3 + hts_md5_hex@Base 1.3 + hts_md5_init@Base 1.3 + hts_md5_reset@Base 1.3 + hts_md5_update@Base 1.3 + hts_open@Base 1.0 + hts_open_format@Base 1.3 + hts_opt_add@Base 1.3 + hts_opt_apply@Base 1.3 + hts_opt_free@Base 1.3 + hts_parse_decimal@Base 1.3 + hts_parse_format@Base 1.3 + hts_parse_opt_list@Base 1.3 + hts_parse_reg@Base 1.0 + hts_readlines@Base 1.0 + hts_readlist@Base 1.0 + hts_set_fai_filename@Base 1.0 + hts_set_opt@Base 1.2.1 + hts_set_threads@Base 1.0 + hts_useek@Base 1.0 + hts_utell@Base 1.0 + hts_verbose@Base 1.0 + hts_version@Base 1.0 + hwrite2@Base 1.0 + int32_decode@Base 1.0 + int32_encode@Base 1.0 + int32_get_blk@Base 1.3 + int32_put_blk@Base 1.3 + is_directory@Base 1.0 + is_file@Base 1.0 + itf8_bytes@Base 1.3 + itf8_decode@Base 1.0 + itf8_decode_crc@Base 1.3 + itf8_encode@Base 1.0 + itf8_put_blk@Base 1.0 + kf_betai@Base 1.0 + kf_erfc@Base 1.0 + kf_gammap@Base 1.0 + kf_gammaq@Base 1.0 + kf_lgamma@Base 1.0 + kftp_connect@Base 1.0 + kftp_connect_file@Base 1.0 + kftp_parse_url@Base 1.0 + kftp_reconnect@Base 1.0 + kgetline@Base 1.3 + kh_clear_s2i@Base 1.0 + kh_del_s2i@Base 1.0 + kh_destroy_s2i@Base 1.0 + kh_get_s2i@Base 1.0 + kh_init_s2i@Base 1.0 + kh_put_s2i@Base 1.0 + kh_resize_s2i@Base 1.0 + khttp_connect_file@Base 1.0 + khttp_parse_url@Base 1.0 + kmemmem@Base 1.0 + knet_close@Base 1.0 + knet_dopen@Base 1.0 + knet_open@Base 1.0 + knet_read@Base 1.0 + knet_seek@Base 1.0 + ks_combsort__off@Base 1.0 + ks_destroy@Base 1.0 + ks_getuntil2@Base 1.0 + ks_heapadjust__off@Base 1.0 + ks_heapmake__off@Base 1.0 + ks_heapsort__off@Base 1.0 + ks_init@Base 1.0 + ks_introsort__off@Base 1.0 + ks_ksmall__off@Base 1.0 + ks_mergesort__off@Base 1.0 + ks_shuffle__off@Base 1.0 + ksplit_core@Base 1.0 + ksprintf@Base 1.0 + kstrnstr@Base 1.0 + kstrstr@Base 1.0 + kstrtok@Base 1.0 + kt_fisher_exact@Base 1.0 + kvsprintf@Base 1.0 + ltf8_decode@Base 1.0 + ltf8_decode_crc@Base 1.3 + ltf8_get@Base 1.0 + ltf8_put@Base 1.0 + mfascii@Base 1.0 + mfclose@Base 1.0 + mfcreate@Base 1.0 + mfcreate_from@Base 1.0 + mfdestroy@Base 1.0 + mfdetach@Base 1.0 + mfeof@Base 1.0 + mfflush@Base 1.0 + mfgetc@Base 1.0 + mfgets@Base 1.0 + mfmmap@Base 1.3 + mfopen@Base 1.0 + mfprintf@Base 1.0 + mfread@Base 1.0 + mfrecreate@Base 1.0 + mfreopen@Base 1.0 + mfseek@Base 1.0 + mfsteal@Base 1.0 + mftell@Base 1.0 + mftruncate@Base 1.0 + mfwrite@Base 1.0 + mkdir_prefix@Base 1.0 + mrewind@Base 1.0 + mstderr@Base 1.0 + mstdin@Base 1.0 + mstdout@Base 1.0 + mungetc@Base 1.0 + open_path_mfile@Base 1.0 + paranoid_fclose@Base 1.0 + pool_alloc@Base 1.0 + pool_create@Base 1.0 + pool_destroy@Base 1.0 + pool_free@Base 1.0 + rans_compress@Base 1.2.1 + rans_compress_O0@Base 1.2.1 + rans_compress_O1@Base 1.2.1 + rans_uncompress@Base 1.2.1 + rans_uncompress_O0@Base 1.2.1 + rans_uncompress_O1@Base 1.2.1 + refs2id@Base 1.0 + refs_free@Base 1.0 + regidx_destroy@Base 1.2.1 + regidx_init@Base 1.2.1 + regidx_insert@Base 1.2.1 + regidx_nregs@Base 1.2.1 + regidx_overlap@Base 1.2.1 + regidx_parse_bed@Base 1.2.1 + regidx_parse_tab@Base 1.2.1 + regidx_seq_names@Base 1.2.1 + regidx_seq_nregs@Base 1.2.1 + sam_format1@Base 1.0 + sam_hdr_PG_ID@Base 1.0 + sam_hdr_add@Base 1.0 + sam_hdr_add_PG@Base 1.0 + sam_hdr_add_lines@Base 1.0 + sam_hdr_decr_ref@Base 1.0 + sam_hdr_dump@Base 1.0 + sam_hdr_dup@Base 1.0 + sam_hdr_find@Base 1.0 + sam_hdr_find_key@Base 1.0 + sam_hdr_find_line@Base 1.0 + sam_hdr_find_rg@Base 1.0 + sam_hdr_free@Base 1.0 + sam_hdr_incr_ref@Base 1.0 + sam_hdr_length@Base 1.0 + sam_hdr_link_pg@Base 1.0 + sam_hdr_name2ref@Base 1.0 + sam_hdr_new@Base 1.0 + sam_hdr_parse@Base 1.0 + sam_hdr_parse_@Base 1.0 + sam_hdr_read@Base 1.0 + sam_hdr_rebuild@Base 1.0 + sam_hdr_sort_order@Base 1.3 + sam_hdr_str@Base 1.0 + sam_hdr_update@Base 1.0 + sam_hdr_vadd@Base 1.0 + sam_hdr_write@Base 1.0 + sam_index_build2@Base 1.3 + sam_index_build@Base 1.3 + sam_index_load2@Base 1.3 + sam_index_load@Base 1.0 + sam_itr_queryi@Base 1.0 + sam_itr_querys@Base 1.0 + sam_open_mode@Base 1.0 + sam_open_mode_opts@Base 1.3 + sam_parse1@Base 1.0 + sam_read1@Base 1.0 + sam_write1@Base 1.0 + seq_nt16_int@Base 1.2.1 + seq_nt16_str@Base 1.0 + seq_nt16_table@Base 1.0 + string_alloc@Base 1.0 + string_dup@Base 1.0 + string_ndup@Base 1.0 + string_pool_create@Base 1.0 + string_pool_destroy@Base 1.0 + stringify_argv@Base 1.0 + t_pool_delete_result@Base 1.0 + t_pool_destroy@Base 1.0 + t_pool_dispatch2@Base 1.0 + t_pool_dispatch@Base 1.0 + t_pool_flush@Base 1.0 + t_pool_init@Base 1.0 + t_pool_next_result@Base 1.0 + t_pool_next_result_wait@Base 1.0 + t_pool_results_queue_empty@Base 1.0 + t_pool_results_queue_len@Base 1.0 + t_pool_results_queue_sz@Base 1.0 + t_results_queue_destroy@Base 1.0 + t_results_queue_init@Base 1.0 + tbx_conf_bed@Base 1.0 + tbx_conf_gff@Base 1.0 + tbx_conf_psltbl@Base 1.0 + tbx_conf_sam@Base 1.0 + tbx_conf_vcf@Base 1.0 + tbx_destroy@Base 1.0 + tbx_index@Base 1.0 + tbx_index_build2@Base 1.3 + tbx_index_build@Base 1.0 + tbx_index_load2@Base 1.3 + tbx_index_load@Base 1.0 + tbx_name2id@Base 1.0 + tbx_parse1@Base 1.0 + tbx_readrec@Base 1.0 + tbx_seqnames@Base 1.0 + tbx_set_meta@Base 1.0 + tokenise_search_path@Base 1.0 + vcf_format@Base 1.0 + vcf_hdr_read@Base 1.0 + vcf_hdr_write@Base 1.0 + vcf_parse@Base 1.0 + vcf_read@Base 1.0 + vcf_write@Base 1.0 + vcf_write_line@Base 1.0 + vflen@Base 1.0 + zfclose@Base 1.0 + zfeof@Base 1.0 + zfgets@Base 1.0 + zfopen@Base 1.0 + zfpeek@Base 1.0 + zfputs@Base 1.0 + zfseeko@Base 1.0 + zftello@Base 1.0 + zlib_mem_inflate@Base 1.0 diff --git a/patches/define_PATH_MAX.patch b/patches/define_PATH_MAX.patch new file mode 100644 index 0000000..5bfd09a --- /dev/null +++ b/patches/define_PATH_MAX.patch @@ -0,0 +1,37 @@ +Author: Andreas Tille , + Svante Signell +Last-Uudate: Wed, 31 Aug 2016 12:14:45 +0200 +Bug-Debian: https://bugs.debian.org/793512 + https://bugs.debian.org/836190 +Description: Define PATH_MAX as it is done in cram/open_trace_file.c if + not existent. The definition should be removed from this C file since the + header file affects all three C files where this definition is used. + +--- a/cram/os.h ++++ b/cram/os.h +@@ -153,6 +153,13 @@ extern "C" { + + #endif + ++/* ++ * in case PATH_MAX is not defined (like in hurd) ++ */ ++#ifndef PATH_MAX ++# define PATH_MAX 1024 ++#endif ++ + /*----------------------------------------------------------------------------- + * Allow for unaligned memory access. This is used in BAM code as the packed + * structure has 4-byte cigar ints after the variable length name. +--- a/cram/open_trace_file.c ++++ b/cram/open_trace_file.c +@@ -72,9 +72,6 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE + #include + #include + #include "cram/os.h" +-#ifndef PATH_MAX +-# define PATH_MAX 1024 +-#endif + + #include "cram/open_trace_file.h" + #include "cram/misc.h" diff --git a/patches/literal_version.patch b/patches/literal_version.patch new file mode 100644 index 0000000..be9c8e2 --- /dev/null +++ b/patches/literal_version.patch @@ -0,0 +1,16 @@ +Description: do not use make to extract version + Without a valid config.mk, trying to call m4_esyscmd_s() to run + make results in weird error messages. This patch avoids having + to run make just to extract this value. +Author: Sascha Steinbiss +--- a/configure.ac ++++ b/configure.ac +@@ -23,7 +23,7 @@ + # DEALINGS IN THE SOFTWARE. + + dnl Process this file with autoconf to produce a configure script +-AC_INIT([HTSlib], m4_esyscmd_s([make print-version]), ++AC_INIT([HTSlib], m4_esyscmd_s([grep 'PACKAGE_VERSION =' Makefile | cut -f 2 -d'=' | xargs]), + [samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/]) + AC_PREREQ(2.63) dnl This version introduced 4-argument AC_CHECK_HEADER + AC_CONFIG_SRCDIR(hts.c) diff --git a/patches/series b/patches/series new file mode 100644 index 0000000..3c1f11a --- /dev/null +++ b/patches/series @@ -0,0 +1,2 @@ +define_PATH_MAX.patch +literal_version.patch diff --git a/rules b/rules new file mode 100755 index 0000000..3480356 --- /dev/null +++ b/rules @@ -0,0 +1,38 @@ +#!/usr/bin/make -f + +# export DEB_BUILD_MAINT_OPTIONS = hardening=+all # Build fails due to -fpie +export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow + +export DH_VERBOSE=1 +DEB_VERSION := $(shell dpkg-parsechangelog | egrep '^Version:' | cut -f 2 -d ' ') + +%: + dh $@ --parallel + +override_dh_auto_test: + dh_auto_test + $(RM) test/*.tmp test/*.tmp.* test/*.o test/*.dSYM \ + test/fieldarith test/hfile test/test_view test/test-vcf-api test/test-vcf-sweep + +override_dh_auto_configure: + autoconf + ./configure --enable-libcurl + +override_dh_auto_build: + dh_auto_build -- \ + CFLAGS="$$(dpkg-buildflags --get CFLAGS)" \ + CPPFLAGS="-I. -DSAMTOOLS=1 $$(dpkg-buildflags --get CPPFLAGS)" \ + LDFLAGS="$$(dpkg-buildflags --get LDFLAGS)" \ +# re-try later LDLIBS=-lhts \ + PACKAGE_VERSION="$(DEB_VERSION)" \ + libdir=/usr/lib/$(DEB_HOST_MULTIARCH) + +override_dh_auto_install: + rm $(CURDIR)/test/sam $(CURDIR)/test/test-regidx + dh_auto_install -- \ + prefix=/usr \ + libdir=/usr/lib/$(DEB_HOST_MULTIARCH) \ + PACKAGE_VERSION="$(DEB_VERSION)" + +override_dh_installchangelogs: + dh_installchangelogs NEWS diff --git a/source/format b/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/source/options b/source/options new file mode 100644 index 0000000..9511377 --- /dev/null +++ b/source/options @@ -0,0 +1,2 @@ +single-debian-patch +extend-diff-ignore = "^(\.travis\.yml|README.md)$" diff --git a/tabix.install b/tabix.install new file mode 100644 index 0000000..431c734 --- /dev/null +++ b/tabix.install @@ -0,0 +1,2 @@ +tabix usr/bin +bgzip usr/bin diff --git a/tabix.links b/tabix.links new file mode 100644 index 0000000..743712c --- /dev/null +++ b/tabix.links @@ -0,0 +1 @@ +usr/share/man/man1/tabix.1.gz usr/share/man/man1/bgzip.1.gz diff --git a/tabix.lintian-overrides b/tabix.lintian-overrides new file mode 100644 index 0000000..ae52d46 --- /dev/null +++ b/tabix.lintian-overrides @@ -0,0 +1,3 @@ +# False positive +spelling-error-in-binary usr/bin/bgzip compres compress +spelling-error-in-binary usr/bin/tabix compres compress diff --git a/tabix.manpages b/tabix.manpages new file mode 100644 index 0000000..bb616e0 --- /dev/null +++ b/tabix.manpages @@ -0,0 +1 @@ +tabix.1 diff --git a/tests/control b/tests/control new file mode 100644 index 0000000..d2aa55a --- /dev/null +++ b/tests/control @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr diff --git a/tests/run-unit-test b/tests/run-unit-test new file mode 100644 index 0000000..314636e --- /dev/null +++ b/tests/run-unit-test @@ -0,0 +1,19 @@ +#!/bin/bash +set -e + +pkg="htslib" + +if [ "$AUTOPKGTEST_TMP" = "" ] ; then + AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` +fi + +cp -a /usr/share/${pkg}-test/* $AUTOPKGTEST_TMP + +cd $AUTOPKGTEST_TMP + +sed -i 's#\$(HTSPREFIX)#/usr/include/#g' htslib_vars.mk +sed -i 's#\$(HTSLIB)#/usr/include/#g' htslib.mk + +make check -j4 + +echo "PASS" diff --git a/upstream/tabix.edam b/upstream/tabix.edam new file mode 100644 index 0000000..6a11cf6 --- /dev/null +++ b/upstream/tabix.edam @@ -0,0 +1,16 @@ +ontology: EDAM (1.13) +topic: + - Sequencing + - Data management +scopes: + - name: summary + function: + - Indexing + inputs: + - data: Sequence coordinates + formats: [TSV, BED, GFF] + - data: Data + formats: [TSV] + outputs: + - data: Data index + formats: [Tabix index file format] diff --git a/watch b/watch new file mode 100644 index 0000000..328a1d9 --- /dev/null +++ b/watch @@ -0,0 +1,3 @@ +version=3 +opts=filenamemangle=s/.+\/v?(\d\S*)\.tar\.gz/htslib-$1.tar.gz/,uversionmangle=s/-rc/~rc/ \ + https://github.com/samtools/htslib/tags .*/v?(\d\S*)\.tar\.gz -- 2.30.2